Greetings, I've been following the "design with non-canonical aa" demo (located on demos/public/design_with_ncaa) in order to set parameters for a custom residue "CYM", which is a deprotonated cysteine. Yet I got stuck in the last step namely, when I try to convert my modified .mol file to params using:
"python molfile_to_params_polymer.py cym.mol --clobber --polymer --no-pdb --name CYM -k cym.kin"
"Traceback (most recent call last):
File "../../Rosetta/demos/public/design_with_ncaa/scripts/python/apps/publi//molfile_to_params_polymer.py", line 1995, in <module>
File "../../Rosetta/demos/public/design_with_ncaa/scripts/python/apps/public/molfile_to_params_polymer.py", line 1953, in main
polymer_assign_pdb_like_atom_names_to_sidechain( m.atoms, m.bonds, options.peptoid )
File "../../Rosetta/demos/public/design_with_ncaa/scripts/python/apps/public/molfile_to_params_polymer.py", line 1697, in polymer_assign_pdb_like_atom_names_to_sidechain
a.pdb_greek_dist = greek_alphabet[all_all_dist[ca_index][i]]
TypeError: list indices must be integers, not float"
But if I skip the --polymer flag, it actually converts my .mol file, but it is defined as ligand and is not recognized by Rosetta.
The same error was already posted ( https://www.rosettacommons.org/node/3763 ), but the source of the problem seems unrelated to my case, as CYM is a Cys-like residue without obvious connection issues that could cause the failure.
I would really appreciate any help you can give me to solve this error.
The .mol file being used as imput is attached as a .txt file.